Results of studies of the sorption activity of diatomite nanoparticles, diatomite–perlite composite nanoparticles and perlite nanoparticles that was provided from internal resource at Iran, with respect to Fe(II), Cu(II), Mn(II) and Cr(III) ions are presented. Thus, diatomite nanoparticles, diatomite–perlite composite nanoparticles and perlite nanoparticles were modified and prepared via particle size decreasing and characterized by XRD, XRF, BET, SEM, TEM and FT-IR. In the batch system the influence of pH, adsorbent dosage, temperature and ions initial concentration was investigated. The results of isotherm and kinetics studies show that the Langmuir isotherm and pseudo-second order kinetic showed better correlation with the experimental data. Calculations of thermodynamic parameters show the negative ΔG° values or spontaneous reaction, the enthalpy (ΔH°) change shows the endothermic process and values of ΔS° indicate low randomness at the solid/solution interface during the uptake of ions. Finally, three adsorbents were packed inside a glass column as a continuous system and the breakthrough curves were obtained. All results show that the ion affinity to adsorption onto adsorbents is as follows: Cu(II) > Fe(II) > Mn(II) > Cr(III). So, these abundant, locally available cheap minerals showed a greater efficiency for the removal of metal ions from the aqueous solution, also can be utilized for other water pollutants.